PXD045318 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Improved detection and quantitation of RNA-interactome using DIA SILAC |
Description | Detection and quantitation of the RNA-interacting proteome is commonly achieved applying SILAC labeling, following by data-dependent acquisition (DDA) of the proteomic data. However, the limited sensitivity of the DDA approach often restricts protein detection to those with higher expression in cells, necessitating peptide fractionation prior to mass spectrometry. Here we report a pipeline for SILAC analysis using data-independent acquisition (DIA), with a spectral library constructed using gas-phase window separation of light materials followed by in silico prediction of heavy spectra. The resulting DIA datasets had 30-40% more detected proteins compared to the same biological materials analyzed using DDA, while abolishing the requirement for pre-MS reverse-phase fractionation of peptides. Lower inter-replicate variations were seen with DIA for proteins detected in both acquisitions. As a test, we determined the effects of arsenite treatment on the RNA-bound proteome of HEK cells recovered following total RNA-associated proteome purification (TRAPP). The DIA dataset yielded clear GO term enrichment for RNA-binding proteins involved in cellular stress responses, while enrichment in the DDA dataset was relatively weak. Dataset normalization of with Cyclic Loess slightly improved the DDA-DIA correlation over median normalization for DIA datasets, but not for DDA dataset relative to default MaxQuant normalization. Overall, the DIA SILAC approach improved both protein detection and biological significance over conventional DDA SILAC. |
HostingRepository | PRIDE |
AnnounceDate | 2023-12-19 |
AnnouncementXML | Submission_2023-12-19_01:50:17.554.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Thomas Tan |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-09-12 10:40:28 | ID requested | |
⏵ 1 | 2023-12-19 01:50:17 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: HEK cells, DIA-SILAC,RNA-interactome |
Contact List
David Tollervey |
contact affiliation | University of Edinburgh |
contact email | d.tollervey@ed.ac.uk |
lab head | |
Thomas Tan |
contact affiliation | University of Edinburgh |
contact email | TCJTAN@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/12/PXD045318 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD045318
- Label: PRIDE project
- Name: Improved detection and quantitation of RNA-interactome using DIA SILAC